no, skillchain damage is not affected by magic defense, only resistances and straight mdt, and the resistances need to be quite high for them to do anything negative. lv3 damage mirrors the closing WS damage plus magic damage+ and 16% for SC bonus III, it's then multiplied further based on its place in the chain and its level.
2step 100%, 3step 150%, 4step 175%, 5step 200%, 6step 225%
Allies roll adds a further multiplier. SAM has 16% on its own, adding a 3 would make it 36% and adding an 11 would make it 41%.
So final SC damage = (ClosingWSDmg * (SClvl/stepmultiplier) * (1 + SCbonus/100) + Magic Damage)
a lv 3 SC thats 4th step off of a 5k WS would look like this:
5000 * 1.75 * (1 + 41/100)
5000 * 1.75 * 1.41 = 12337 damage before resistance and ilvl bonus
Ilvl and mob resistance is factored in like so:
http://www.bluegartr.com/threads/108199-Random-Facts-Thread-Other?p=6144154&viewfull=1#post6144154
12337 * 1.3 = 16038 final 4th step SC damage on a target with no MDT-
for a 6th step SC:
5000 * 2.25 * 1.41 = 15862
15862 * 1.3 = 20620
With Sengikori:
5000 * 2.25 * 1.41 * 1.25 = 19828
19828 * 1.3 = 25776
higher damage WS:
7500 * 2.25 * 1.41 * 1.25 = 29742
29742 * 1.3 = 38664
needless to say, you get much more out of 5stepping your SCs with SC bonus than you would 2step SCing over and over again with slightly stronger WSs (assuming your attack isn't so low that Chaos is raising your WS dmg output by 3k+, in which case I'm not sure). The cumulative bonus in SC damage over the course of 5 SCs in a single chain is quite a massive increase in damage.
99k on Wopket can be reproduced with +50% damage from monster weakness and a strong Koga enhanced Fudo on a slashing weak monster. iirc SC Bonus caps at 50%, but I'm not sure if that's still the case.
If someone wants to correct something here feel free, some newer testing may have indicated something different than what's written here.